Molecular Epidemiology Section

The Molecular Epidemiology laboratory provides molecular-based testing to widen the range of laboratory capacity for rapidly identifying emerging pathogens. This laboratory provides cutting edge technology that enhances efforts in characterizing infectious diseases. It implements the tools that provide information for surveillance initiatives and serves as the hallmark for investigative and control aspects of infectious diseases of public health importance.

Molecular based methodologies offer a unique combination of extraordinary sensitivity and reproducibility due to the fact that the target molecules, such as deoxyribose nucleic acid (DNA) and ribose nucleic acid (RNA), are typically not altered by laboratory manipulations. Molecular techniques used for testing are not necessarily dependent on cellular functions or protein expression. Therefore, molecular techniques can lead to more precise identification of pathogens, since the organisms can be characterized at the subspecies or strain level. In other instances, molecular techniques provide a powerful means for detecting infectious agents that would otherwise remain unrecognized by conventional testing methods. The combined use of molecular and conventional techniques provide physicians and health care workers with invaluable information that directly affects the treatment and care of South Carolinians throughout the state.

Molecular techniques utilized:

Polymerase Chain Reaction

Polymerase chain reaction (PCR) is a simple, elegant tool for amplifying a specific nucleic acid sequence of DNA or RNA until there is enough material to detect and identify. Testing for qualitative DNA for HIV-1 and Bordetella pertussis are two molecular based PCR assays currently performed.

Qualitative HIV-1 DNA testing
Human immunodeficiency virus (HIV) is the causative agent of Acquired Immune Deficiency Syndrome (AIDS). Early detection of the virus is critical for proper treatment and management of the disease. Detection of HIV-1 DNA by PCR is useful for the diagnosis of very early, post-exposure HIV infection in the window period prior to the production of antibodies (seroconversion). PCR allows the exponential amplification of a nucleic acid sequence in the HIV proviral DNA which is particularly important due to the low number of infected lymphocytes in a patient. The usefulness of this assay includes:

Bordetella pertussis DNA testing.
Pertussis continues to infect many people worldwide and remains a significant public health problem. Newly developed molecular technology, such as PCR, has increased detection sensitivity of a small number of bacteria and has considerably reduced analysis turnaround time. Bordetella pertussis (Whooping cough) can now be detected from clinical respiratory or nasopharyngeal swab specimens by polymerase chain reaction amplification in less than 2 days of assay time.

Pulsed Field Gel Electrophoresis

Detection and identification of microorganisms, such as bacteria, from clinical specimens is critical to maintaining the good health of our community. It is often crucial to determine the relatedness of a group of bacterial isolates such that their epidemiologic relationships can be established. One technique, pulsed field gel electrophoresis (PFGE), can provide this information on a molecular level.

In PFGE, the chromosomal DNA of each isolate is digested with specific restriction enzymes that cut the DNA into fragments that vary in length. The fragments are then separated by size to create a genetic “fingerprint” that is distinct to that isolate. Isolates that are collected from the same site or “outbreak” are then compared to one another to determine relatedness. Strains that have the same “fingerprint” pattern are said to be related or closely related. This information is very useful in identifying the source of contamination or infection and it may impact on how an outbreak is resolved. PFGE results are highly reproducible and discriminatory and can be applied to a wide range of organisms.

This illustration of PFGE depicts DNA fingerprints from a Foodborne pathogen, Staphylococcus aureus, outbreak. In this dendrogram, DNA fingerprints show the strain in the dressing to be indistinguishable from the Staph cultured from the turkey, ham and employee B. Also, the Staphylococcus aureus grown from the barbecue pork, grilled chicken, a nasal isolate and a hand wound isolate cultured from employee A were all indistinguishable.

The Molecular Epidemiology laboratory is a participating PulseNet laboratory, which is the CDC based national computer network for detection and intervention of Foodborne illnesses . It is through the efforts of the PulseNet that Foodborne pathogen DNA fingerprints, provided to the national database by the participating PulseNet laboratories, can be compared on a nationwide basis. This state-to-state network provides rapid implementation of prevention and intervention measures in the case of an outbreak situation. Thus, allowing the Molecular Epidemiology laboratory to support food safety initiatives for the state.